Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
POU2F2

Cell type

Cell type Class
Blood
Cell type
OCI-LY-7
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
OCI-Ly7
treatment
control_sgRNA
cell line
OCI-Ly7
knock down
control
chip antibody
OCT2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10 million cells were fixed in 1% formaldehyde for 10 min at room temperature, and fragmentation of fixed chromatin was obtained from isolated nuclei by sonication. To enrich for short chromatin fragments (200 - 700 bp), 5μg of antibody was added to the chromatin lysate and incubated overnight at 4 °C. The following day, Dynabeads protein A was added and incubated with rotation at 4 °C for 1.5 hours. Enriched DNA was isolated through extensive wash steps, subsequent reverse cross-linking, and purification using DNA Clean & Concentrator Kit. ChIP-seq libraries were prepared from 2-5 ng ChIP DNA. After end-repair, A-tailing, and ligation with barcodes, barcoded DNA was amplified by 12 cycles of PCR using Phusion® High-Fidelity DNA Polymerase. 50bp single-end.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
49632275
Reads aligned (%)
98.5
Duplicates removed (%)
13.7
Number of peaks
45522 (qval < 1E-05)

hg19

Number of total reads
49632275
Reads aligned (%)
98.0
Duplicates removed (%)
14.3
Number of peaks
45399 (qval < 1E-05)

Base call quality data from DBCLS SRA